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518 results for “cycling data”
Data from: Rapid-cycling Brassica rapa evolves even earlier flowering under experimental drought
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Data from: Transgression-regression cycles drive correlations in Ediacaran-Cambrian rock and fossil records
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Redwood Creek Chinook salmon life cycle model code and data
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Data for: Brain activity of diving seals reveals short sleep cycles at depth
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Soil Microbial and N cycling data along a wetland plant community gradient
This dataset contains soil chemical and microbial data taken from surface soil cores (15cm) from the Black Spruce, Willow/Birch, Tussock, Emergent Fen, and Rich Fen plant communities along the APEX boardwalk. Data include DOC, soil C, potential nitrification, potential denitrification, soil DNA concentration, water content, ammonium concentration, nitrate concentration, archaea abundance, NirK functional gene abundance, ammonia oxidizing bacteria (AOB) abundance, ammonia oxidizing archaea (AOA) abundance, NosZ functional gene abundance, and eubacteria abundance.
Data from: Tradeoffs with growth limit host range in complex life cycle helminths
Parasitic worms with complex life cycles have several developmental stages, with each stage creating opportunities to infect additional host species. Using a dataset for 973 species of trophically transmitted acanthocephalans, cestodes, and nematodes, we confirmed that worms with longer life cycles (i.e. more successive hosts) infect a greater diversity of host species and taxa (after controlling for study effort). Generalism at the stage level was highest for 'middle' life stages, the second and third intermediate hosts of long life cycles. By simulating life cycles in real food webs, we found that middle stages had more potential host species to infect, suggesting that opportunity constrains generalism. However, parasites usually infected fewer host species than expected from simulated cycles, suggesting generalism also has costs. There was no tradeoff in generalism from one stage to the next, but worms spent less time growing and developing in stages where they infected more taxonomically diverse hosts. Our results demonstrate that life cycle complexity favors high generalism, and host use across life stages is determined by both ecological opportunity and life history tradeoffs.
Data from: Soils from cold and snowy temperate deciduous forests release more nitrogen and phosphorus after soil freeze–thaw cycles than soils from warmer, snow-poor conditions
<p>Effects of global warming are most pronounced in winter. A reduction in snow cover due to warmer atmospheric temperature in formerly cold ecosystems, however, could counteract an increase in soil temperature by reduction of insulation. Thus, soil freeze-thaw cycles (FTC) might increase in frequency and magnitude with warming, potentially leading to a disturbance of the soil biota and release of nutrients.</p> <p>Here, we assessed how soil freeze-thaw magnitude and frequency affect short-term release of nutrients in temperate deciduous forest soils by conducting a three factorial gradient experiment with ex-situ soil samples in climate chambers. The fully-crossed experiment included soils from forests dominated by <i>Fagus sylvatica</i> (European beech) that originate from different winter climate (mean coldest month temperature range ΔT > 4 K), a range of FTC magnitudes from no (T = 4.0 °C) to strong (T = -11.3 °C) soil frost, and a range of FTC frequencies (f = 0–7). We hypothesized that higher FTC magnitude and frequency, respectively, will increase the release of nutrients. Furthermore, soils from cold climates with historically stable winter soil temperatures due to deep snow cover will be more responsive to FTC than soils from warmer, more fluctuating winter soil climates.</p> <p>FTC magnitude and, to a lesser extent, also FTC frequency resulted in increased nitrate, ammonium, and phosphate release almost exclusively in soils from cold, snow-rich sites. The hierarchical regression analyses of our three-factorial gradient experiment revealed that the effects of climatic origin (mean minimum winter temperature) followed a sigmoidal curve for all studied nutrients and was modulated either by FTC magnitude (phosphate) or by FTC magnitude and frequency (nitrate, ammonium) in complex two- and, for all studied nutrients, in threefold interactions of the environmental drivers. Compared to initial concentrations, soluble nutrients were predicted to increase to 250 % for nitrate (up to 16 µg NO<sub>3</sub>-N kg<sup>-1</sup>DM), to 110 % for ammonium (up to 60 µg NH<sub>4</sub>-N kg<sup>-1</sup>DM), and to 400 % for phosphate (2.2 µg PO<sub>4</sub>-P kg<sup>-1</sup>DM) at the coldest site for strongest magnitude and highest frequency. Soils from warmer sites showed little nutrient release and were largely unaffected by the FTC treatments except for above-average nitrate release at the warmest sites in response to extremely cold FTC magnitude.</p> <p>We suggest that currently warmer forest soils have historically already passed the point of high responsiveness to winter climate change, displaying some form of adaptation either in the soil biotic composition or in labile nutrient sources. Our data suggests that previously cold sites, which will lose their protective snow cover during climate change, are most vulnerable to increasing FTC frequency and magnitude, resulting in strong shifts in nitrogen and phosphorus release. In nutrient poor European beech forests of the studied Pleistocene lowlands, nutrients released over winter may be leached out, inducing reduced plant growth rates in the following growing season.</p> <p>Here, we provide the raw data of a three-factorial regression experiment and the R-Code used in the hierarchical regression analysis of this raw data in Kreyling et al.: Soils from cold and snowy temperate deciduous forests release more nitrogen and phosphorus after soil freeze-thaw cycles than soils from warmer, snow-poor conditions.</p>
Data from: Cycles of trans‐Arctic dispersal and vicariance, and diversification of the amphi‐boreal marine fauna
<p>The amphi‐boreal faunal element comprises closely related species and conspecific populations with vicarious distributions in the North Atlantic and North Pacific basins. It originated from an initial trans‐Arctic dispersal in the Pliocene after the first opening of the Bering Strait, and subsequent vicariance through the Pleistocene when the passage through the Arctic was severed by glaciations and low sea levels. Opportunities for further dispersal have risen at times however, and molecular data now expose more complex patterns of inter‐oceanic affinities and dispersal histories. For a general view on the trans‐Arctic dynamics and of the roles of potential dispersal‐vicariance cycles in generating systematic diversity we produced new phylogeographic data sets for amphi‐boreal taxa in 21 genera of invertebrates and vertebrates, and combined them with similar published data sets of mitochondrial coding gene variation, adding up to 89 comparisons involving molluscs, crustaceans, echinoderms, polychaetes, fishes and mammals. Only 39% of the cases correspond with a simple history of Pliocene divergence; in most taxonomical groups, the range of divergence estimates implies connections through the entire Pliocene–Pleistocene‐Holocene time frame. Repeated inter‐oceanic exchange was inferred for 23 taxa, and the latest connection was usually post‐glacial. Such repeated invasions have usually led to secondary contacts and occasionally to widespread hybridization between the different invasion waves. Late‐ or post‐glacial exchange was inferred in 50% of the taxa, stressing the importance of the relatively recent invasions to the current diversity in the Northern Atlantic. Individual taxa also showed complex idiosyncratic patterns and histories, and several instances of cryptic speciation were recognized. In contrast to a simple inter‐oceanic vicariance scenario underlying amphi‐boreal speciation, the data expose complex patterns of reticulation and introgression that complicate the interpretation of taxon boundaries in the region.</p>
Supplemental Data for "The Sensitivity of Eyewall Replacement Cycles to Shortwave Radiation"
<p>The repository contains files to reproduce the simulations and analyses described in the manuscript "The Sensitivity of Eyewall Replacement Cycles to Shortwave Radiation" which has been published in the Journal of Geophysical Research: Atmospheres and can be found at <a href="https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020JD034016">https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020JD034016</a>. Model configuration can also be found at <a href="https://doi.org/10.1175/JAS-D-18-0165.1">https://doi.org/10.1175/JAS-D-18-0165.1</a></p> <p> </p> <p><strong>Includes</strong></p> <p>input_sounding ----- Initial thermodynamic profile to initialize WRF</p> <p>namelist.input ----- Set of input parameters to run WRF</p> <p>wrfrst_* ----- WRF restart files for the 3 domains for two times (July 7 (96h restart) and July 5 (48h restart)</p> <p> </p>
FIB-tomography data of Ni-YSZ anodes for Solid Oxide Fuel Cells (SOFC): Comparison of pristine and degraded materials (before/after redox cycling)
<p><em>Contents: </em></p> <p>This dataset contains 3D image stacks acquired with FIB-tomography from Ni-YSZ cermet anodes for Solid Oxide Fuel Cells (SOFC).</p> <p>The data was collected from three different Ni-YSZ anodes (fine-, medium- and coarse-grained). Each of these anodes was investigated first in pristine state (after sintering and reduction) and then also in degraded state (after exposure to 8 redox cycles).</p> <p>The 6 tomographs are then presented as stacks of 2D-tiff-images in 2 different versions: as gray-scale images (raw data) and as segmented images (Ni=white, YSZ=gray and pores=black). In total this gives 12 image stacks.</p> <p><strong>Further details</strong>, such as the voxel resolutions and image window sizes are listed in the downloadable excel file (<strong>2_3D_Data_Info.xlsx</strong>).</p> <p> </p> <p><em>Scientific Context: </em></p> <p>The microstructures of the cermet anodes were investigated for the purpose of optimizing the anode performance, which depends on effective transport properties (i.e. conductivity of ions in YSZ and of electrons in Ni, as well as diffusivity of fuel/gas in the pores). Furthermore the anode performance also depends on the catalytic/electrochemical activity (i.e. Ni-surface area and three phase boundary length TPBL). The microstructure characteristics have a strong influence on effective properties, electrochemical activity and associated anode performance. Furthermore, microstructure degradation (e.g. by Ni-coarsening) may lead to performance loss over time.</p> <p>Hence, the investigations focus on a fundamental, quentitative understanding of the relationships between microstructure characteristics and effective properties. The study reveals quantitative descriptions of all relevant microstructure characteristics (porosity, tortuosity, constrictivity, surface/interface areas, TPBL) and of the corresponding effective transport porperties (electric and ionic.conductivities). The corresponding anode performance was characterized by impedance spectroscopy.</p> <p>The quantitative <strong>results of the microstructure investigation were published</strong> in:</p> <p><strong>Pecho et al</strong> 2015a (doi:10.3390/ma8095265),</p> <p><strong>Pecho et al</strong> 2015b (doi:10.3390/ma8105370),</p> <p><strong>Holzer et al</strong> 2013 (doi: 10.1016/j.jpowsour.2013.05.047),</p> <p><strong>Holzer et al</strong> 2011a (doi: 10.1016/j.jpowsour.2010.08.017) and</p> <p><strong>Holzer et al</strong> 2011b (doi: 10.1016/j.jpowsour.2010.08.006).</p>
Data for: Environmental conditions alter behavioural organization and rhythmicity of a large Arctic ruminant across the annual cycle
<p><span>The existence and persistence of rhythmicity in animal activity during phases of environmental change is of interest in ecology and chronobiology. A wide diversity of biological rhythms in response to</span> <span>exogenous </span>conditions and internal stimuli have been uncovered, especially for polar vertebrates. However, empirical data supporting circadian organization of large ruminating herbivores remains inconclusive. <span>Using year-round tracking data of the largest Arctic ruminant, the muskox (</span><i>Ovibos moschatus</i><span>), we modelled rhythmicity as a function of behaviour and environmental conditions. Behavioural states were classified based on patterns in hourly movements, and incorporated within a periodicity analyses framework. We found that ultradian rhythmicity was prevalent when muskoxen were foraging and resting in mid-winter (continuous darkness). However, the probability of rhythmicity declined with increasing photoperiod until largely disrupted in mid-summer (continuous light). Individuals that remained rhythmic during mid-summer foraged in areas with lower plant productivity (NDVI) than arrhythmic individuals. We conclude that muskoxen may use internal time keeping when forage resources are low, but that the importance of this mechanism weakens once environmental conditions allow energetic reserves to be replenished. We argue that alimentary function and metabolic requirements are critical determinants of biological rhythmicity in muskoxen, which likely applies to ruminating herbivores in general. </span></p>
Data for 'Heat stress destabilizes symbiotic nutrient cycling in corals'
<p>Physiological data (tab 1) and NanoSIMS data (tab 2) associated with publication 'Heat stress destabilizes symbiotic nutrient cycling in corals'. </p>
Data from: Burrowing detritivores regulate nutrient cycling in a desert ecosystem
Nutrient cycling in most terrestrial ecosystems is thought to be controlled by moisture-dependent decomposer activity. In arid ecosystems, plant litter cycling exceeds rates predicted based on precipitation amounts, suggesting that additional factors are involved in these systems. Attempts to reveal these factors have predominantly focused on abiotic degradation, precipitation frequency, soil-litter mixing, and alternative moisture sources. Our aim was to explore an additional hypothesis that macro-detritivores control litter cycling in deserts. We quantified the role different organisms play in clearing plant detritus from the desert surface, using litter-baskets with different mesh sizes that allow selective entry of micro-, meso- or macro-fauna. We also measured soil nutrient concentrations in increasing distances from the burrows of a highly abundant macro-detritivore, the desert isopod Hemilepistus reaumuri, in the field and in laboratory microcosms. Macro-detritivores controlled the clearing of plant litter in our field site. The highest rates of litter removal were measured during the hot and dry summer when isopod activity peaks and microbial activity is minimal. We also found substantial enrichment of inorganic nitrogen and phosphorous in the vicinity of isopod burrows. We conclude that burrowing macro-detritivores are important regulators of litter cycling in this arid ecosystem, providing a plausible general mechanism that explains the unexpectedly high rates of plant-litter cycling in deserts.
Data from: Decoupled responses of soil bacteria and their invertebrate consumer to warming, but not freeze-thaw cycles, in the Antarctic Dry Valleys
Altered temperature profiles resulting in increased warming and freeze–thaw cycle (FTC) frequency pose great ecological challenges to organisms in alpine and polar ecosystems. We performed a laboratory microcosm experiment to investigate how temperature variability affects soil bacterial cell numbers, and abundance and traits of soil microfauna (the microbivorous nematode Scottnema lindsayae) from McMurdo Dry Valleys, Antarctica. FTCs and constant freezing shifted nematode body size distribution towards large individuals, driven by higher mortality among smaller individuals. FTCs reduced both bacterial and nematode abundance, but bacterial cell numbers also declined under warming, demonstrating decoupled consumer–prey responses. We predict that higher occurrence of FTCs in cold ecosystems will select for large body size within soil microinvertebrates and overall reduce their abundance. In contrast, warm temperatures without FTCs could lead to divergent responses in soil bacteria and their microinvertebrate consumers, potentially affecting energy and nutrient transfer rates in soil food webs of cold ecosystems.
Data from: Evidence for complex life cycle constraints on salamander body form diversification
Metazoans display a tremendous diversity of developmental patterns, including complex life cycles composed of morphologically disparate stages. In this regard, the evolution of life cycle complexity promotes phenotypic diversity. However, correlations between life cycle stages can constrain the evolution of some structures and functions. Despite the potential macroevolutionary consequences, few studies have tested the impacts of life cycle evolution on broad-scale patterns of trait diversification. Here we show that larval and adult salamanders with a simple, aquatic-only (paedomorphic) life cycle had an increased rate of vertebral column and body form diversification compared to lineages with a complex, aquatic-terrestrial (biphasic) life cycle. These differences in life cycle complexity explain the variations in vertebral number and adult body form better than larval ecology. In addition, we found that lineages with a simple terrestrial-only (direct developing) life cycle also had a higher rate of adult body form evolution than biphasic lineages, but still 10-fold lower than aquatic-only lineages. Our analyses demonstrate that prominent shifts in phenotypic evolution can follow long-term transitions in life cycle complexity, which may reflect underlying stage-dependent constraints.
Data from: Life cycle matters: DNA barcoding reveals contrasting community structure between fern sporophytes and gametophytes
Ferns are the only major lineage of vascular plants that have nutritionally independent sporophyte (diploid) and gametophyte (haploid) life stages. However, the implications of this unique life cycle for fern community ecology have rarely been considered. To compare patterns of community structure between fern sporophytes and gametophytes, we conducted a survey of the ferns of the islands of Moorea and Tahiti (French Polynesia). We first constructed a DNA barcode library (plastid rbcL and trnH–psbA) for the two island floras including 145 fern species. We then used these DNA barcodes to identify more than 1300 field-collected gametophytes from 25 plots spanning an elevational gradient from 200 to 2000 m. We found that species richness of fern sporophytes conforms to the well-known unimodal (i.e., mid-elevation peak) pattern, reaching a maximum at ca. 1000 – 1200 m. Moreover, we found that fern sporophyte communities become increasingly phylogenetically clustered at high elevations. In contrast, species richness of fern gametophytes was consistent across sites, and gametophytes showed no correlation of phylogenetic community structure with elevation. Turnover of sporophyte and gametophyte communities was closely linked with elevation at shallow phylogenetic levels, but not at deeper nodes in the tree. Finally, we found several species for which gametophytes had broader ranges than sporophytes, including a vittarioid fern with abundant gametophytes but extremely rare sporophytes. Our study highlights the importance of including diverse life history stages in surveys of community structure, and has implications for the possible impacts of climate change on the distribution of fern diversity.
Data from: Nitrogen cycling and export in California chaparral: the role of climate in shaping ecosystem responses to fire
Climate change models predict that interannual rainfall variability will increase in California over the next several decades; these changes will likely influence how frequently California ecosystems burn and how they respond to fire. Fires uncouple N mobilization from uptake by destroying plant biomass and increasing nitrification. Following fire, autumn and winter rains can leach N into streams from slopes that have been denuded. The amount of N exported depends on how rapidly soil microbes metabolize it into mobile forms such as NO3-, and the rate that recovering plants take up available N. However, the long-term effects of a changing climate on postfire N dynamics remain unknown. We used the ecohydrologic model RHESSys (regional hydro-ecologic simulation system) to evaluate how interannual climate variability may affect the magnitude of N mineralization, nitrification, N export, and plant recovery following fire. N export was highest when fire was followed by drought; even though there was less water moving through the system, dry conditions prolonged the period during which N mobilization was decoupled from plant uptake. We also found that the effects of drought on N export were magnified in stands dominated by obligate seeders, which initially recovered more slowly than resprouters. These findings suggest that climate may regulate N balance most powerfully by influencing how quickly plants "turn on" and begin to immobilize N.
Data from: Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons
Background: The vaginal microbiome is an important site of bacterial-mammalian symbiosis. This symbiosis is currently best characterized for humans, where lactobacilli dominate the microbial community and may help defend women against infectious disease. However, lactobacilli do not dominate the vaginal microbiota of any other mammal studied to date, raising key questions about the forces that shape the vaginal microbiome in non-human mammals. Results: We used Illumina sequencing of the bacterial 16S rRNA gene to investigate variation in the taxonomic composition of the vaginal microbiota in 48 baboons (Papio cynocephalus), members of a well-studied wild population in Kenya. Similar to prior studies, we found that the baboon vaginal microbiota was not dominated by lactobacilli. Despite this difference, and similar to humans, reproductive state was the dominant predictor of baboon vaginal microbiota, with pregnancy, postpartum amenorrhea, and ovarian cycling explaining 18% of the variance in community composition. Furthermore, among cycling females, a striking 39% of variance in community composition was explained by ovarian cycle phase, with an especially distinctive microbial community around ovulation. Peri-ovulatory females exhibited the highest relative abundance of lactic acid-producing bacteria compared to any other phase, with a mean relative abundance of 44%. To a lesser extent, sexual behavior, especially a history of shared sexual partners, also predicted vaginal microbial similarity between baboons. Conclusions: Despite striking differences in their dominant microbes, both human and baboon vaginal microbiota exhibit profound changes in composition in response to reproductive state, ovarian cycle phase, and sexual behavior. We found major shifts in composition during ovulation, which may have implications for disease risk and conception success. These findings highlight the need for future studies to account for fine-scale differences in reproductive state, particularly differences between the various phases of the ovarian cycle. Overall, our work contributes to an emerging understanding of the forces that explain intra- and inter-individual variation in the mammalian vaginal microbiome, with particular emphasis on its role in host health and disease risk.
Data from: Consequences of breeding system for body condition and survival throughout the annual cycle of tidal marsh sparrows
An individual's body condition and probability of survival can change throughout the annual cycle, based on the combined effects of many factors, including reproductive investment during breeding, colder temperatures during winter, and elevated risks during migration. We evaluated body condition and survival during breeding and non-breeding periods in two closely related species with notably different reproductive systems. Male and female saltmarsh sparrows (Ammodramus caudacutus) represent extremes in parental care: males perform none, leaving females to do everything from build nests to care for fledglings. In contrast, male and female seaside sparrows (A. maritimus) have bi-parental care and similar levels of reproductive investment, intermediate between male and female saltmarsh sparrows. Our results are consistent with the idea that females experience non-lethal effects of reproduction, and that differences between the breeding season and winter affect condition. In both species, females had lower scaled mass index (SMI) values than males during both breeding and non-breeding seasons, and female saltmarsh sparrows had lower SMI values than female seaside sparrows. Females carried more fat than males during the breeding season, and female, but not male, fat and muscle scores decreased over time, which is consistent with the adaptive mass hypothesis. In winter, all groups carried more fat and had higher muscle scores than when breeding, despite having lower SMI scores. Although we observed variation in body condition, within-season survival was uniformly high in both seasons, suggesting that sex, species, season, body size, and body condition have little impacts on within season survival. Comparisons with previously-published estimates of annual adult survival suggest that most mortality occurs during migration, even in these short-distance migrants. The importance of considering multiple aspects of body condition, multiple seasons, and difficult-to-monitor events, such as migration, should not be ignored when thinking about the events and processes that cumulatively determine population dynamics.
Data from: Connecting the dots: Stopover strategies of an intercontinental migratory songbird in the context of the annual cycle
The phases of the annual cycle for migratory species are inextricably linked. Yet, less than five percent of ecological studies examine seasonal interactions. In this study, we utilized stable hydrogen isotopes to geographically link individual black-and-white warblers (Mniotilta varia) captured during spring migration with breeding destinations to understand a migrant's stopover strategy in the context of other phases of the annual cycle. We found that stopover strategy is not only a function of a bird's current energetic state, but also the distance remaining to breeding destination and a bird's time-schedule, which has previously been linked to habitat conditions experienced in the preceding phase of the annual cycle. Birds in close proximity to their breeding destination accumulate additional energy reserves prior to arrival on the breeding grounds, as reflected by higher migratory condition upon arrival, higher refueling rates measured via blood plasma metabolites, and longer stopover durations compared to birds migrating to breeding destinations farther from the stopover site. However, late birds near their breeding destination were more likely to depart on the day of arrival (i.e., transients), and among birds that stopped over at the site, the average duration of stopover was almost half the time of early conspecifics, suggesting late birds are trying to catch-up with the overall time-schedule of migration for optimal arrival time on the breeding grounds. In contrast, birds with long distances remaining to breeding destinations were more likely to depart on the day of arrival and primarily used stopover to rest before quickly resuming migration, adopting similar strategies regardless of a bird's time-schedule. Our study demonstrates that migrants adjust their en route strategies in relation to their time-schedule and distance remaining to their breeding destination, highlighting that strategies of migration should be examined in the context of other phases of the annual cycle.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.